title: LM8_2

city: Lyon

first: joel

last: lachuer

address: 8 avenue rockefeller

country: France

institute: university Lyon1

description:
S4
P+7/LM8-20210524-01

data_processing:
Base calling with NCS 2.0.2 RTA 2.4.11.
Demultiplexing with Bcl2fastq v2.17.1.14 (with 1 mismatch).
Trimming with CutAdapt v1.9.1 (Threshold quality score to 30). Minimum length of 50 bases after trimming. The maximum rate of undetermined bases (“N”s) was set to 0%. Adapters were trimmed with 3 bases overlap, a maximum error rate of 10%.
Alignment using STAR v2.7.9a.
Variant calling (Mutect2 GATK v4.3.0 Somatic short variants discovery pipeline).
Variant annotation (snpEff v5.1d).
Assembly: Mus musculus (GRCm39, Ensembl Release=104).
Supplementary files format and content: MBT2 matrix (format .txt) (containing variant calling for S1 and S2 samples).
Supplementary files format and content: LM8 matrix (format .txt) (containing variant calling for S3 and S4).

growth_protocol: Bladder cancer cell-line MBT2, syngeneic from C3H/HeN strain mice, was derived from kindly provided by Pr. Yves Fradet’s laboratory (Laboratoire d'Uro-Oncologie Expérimentale, Université Laval, Québec, QC, Canada) and cultured in RPMI-1640 (Gibco, #21875-034), supplemented with FBS 10% (Dominique Dutcher, #10270S-181050), and 1% Penicillin/Streptomycin (Gibco, #15140-122). Osteosarcoma cell line LM8 (Creative Bioarray, #CSC-C6376J), syngeneic from C3H/HeN strain mice, was cultured in MEM (Sigma, #M2279), supplemented with FBS 10% (Dominique D utcher, #10270S-181050), and 1% Penicillin/Streptomycin (Gibco, #15140-122) and Hepes at 24mM final concentration (Gibco, #2026999).

extract_protocol:
RNA extraction : RNeasy Micro kit + DNase treatment (Qiagen).
NEXTFLEX® Rapid Directional RNA Seq Kit 2.0 PerkinElmer with NEXTFLEX ® Poly(A) Beads 2.0 PerkinElmer without spike.
Flow cell MidOutput, PE 2x75bp.

value: Osteosarcoma cancer cell line


title: Monomer_GEX

status: Public on May 31 2024

type: SRA

city: Birmingham

first: Yong

last: Wang

state: AL

address: 1918 University Blvd

department: Cell, Developmental and Integrative Biology

country: USA

institute: University of Alabama at Birmingham

description:
10x Genomics
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI, read2 file contains transcript
Monomer_barcodes.tsv
Monomer_features.tsv
Monomer_matrix.mtx

library_source: transcriptomic single cell

data_processing:
Raw base call files were demultiplexed into FASTQ files. Sequencing files were processed and mapped to mm10, and count matrices were extracted using the Cell Ranger Single Cell Software (v 7.1.0) .
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Mus musculus

source_name: midbrain

extract_protocol:
Mononuclear cells were isolated for sequencing as described above with 3-5 ventral midbrains pooled per sample and sorted for CD45+ live cells on a BD FACsAria. Sorted CD45+ cells were resuspended in DPBS supplemented with 0.04% w/v BSA.
Single Cell 3′ Reagent Kit V3.1 was used in conjunction with TotalSeqB antibodies to generate 3' gene expression library and HTO library. Single cells and beads containing barcoded DNA oligos were captured into oil droplets to generate the gel bead-in-emulsion (GEM) by 10x Chromium controller. The poly-A RNA from the cell lysate in GEM was reverse-transcripted to cDNA. Libraries were constructed according to the manufacturer’s instructions

tag: tissue

value: midbrain

tag: cell line

tag: cell type

value: CD45+ cells

tag: genotype

value: Line 61 mice

tag: treatment

value: Monomer

tag: library type

value: mRNA


title: Day3_f3

city: Palo Alto

first: Avnesh

last: Thakor

state: California

address: 3155 Porter Dr

department: Radiology

institute: Stanford Medicine

description:
f03_3
female at day 3

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence,
Then mapped to mouse genome Mus Musculus using HISTAT
HTSeq was used to generate the raw read counts
DESeq2 was used for differential gene expression analysis
Assembly: (GRCm39/mm39)
Supplementary files format and content: tab-delimited text file include FPKM values for all samples
Supplementary files format and content: tab-delimited text file include raw counts for all samples

molecule: total RNA

source_name: kidney

extract_protocol:
total RNA was extracted from each replicate using the RNAeasy minikit (qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

tag: strain

value: wt

tag: Sex

value: female

value: cisplatin

tag: time


title: FTO-1

city: Nanjing

first: Zhang

last: Min

address: Jiangwangmiao Street, Xuanwu District

country: China

institute: Hospital for Skin Diseases

data_processing:
Sequence alignment of Clean Reads to a reference genome using Hisat2 to obtain information on the position on the reference genome or gene, as well as information on sequence features specific to the sequenced sample. Gene transcription generates precursor mRNAs (pre-mRNAs) that are spliced in a variety of ways, selecting different exons to produce different mature mRNAs, which are translated into different proteins, constituting a diversity of biological traits. This post-transcriptional mRNA processing is called variable splicing or selective splicing. StringTie was used to splice the Hisat2 comparison results, and the type of variable splicing present in each sample and the corresponding expression was obtained by ASprofile software.
Assembly: mm10
Supplementary files format and content: All_gene_counts.list

organism: Homo sapiens

source_name: Cell

extract_protocol:
Nucleic acid extraction was accomplished using the (Tengen DP411, CLB + Adderall RN40 CTAB + Adderall RN40, Tengen DP762-T1C) kit/TRIzol reagent.
The first step is to purify and break the mRNA, the second step is to synthesize the first strand of cDNA, the third step is to synthesize the second strand of cDNA and purify the second strand product, the fourth step is to repair the ends and add A to the 3'-ends, the fifth step is to ligate the junctions, the sixth step is to purify the ligated product and select the fragment, the seventh step is to amplify the ligated product, the eighth step is to purify the PCR product, and the final step is to perform a quality check on the library by using the Qsep-400 method.

value: Cell

value: HaCat cells

value: keratinocytes


title: Vector-2


title: PBS_GEX

description:
10x Genomics
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI, read2 file contains transcript
PBS_barcodes.tsv
PBS_features.tsv
PBS_matrix.mtx

value: PBS


title: Day5_m1

description:
m05_1
male at day 5

value: male


title: Vector-1


title: E11_5_CVG_H3K4me3_Rep2

city: Augusta

first: Lin

last: Gan

state: Geogia

address: 1120 15th Street

department: Department of Neuroscience & Regenerative Medicine

institute: Augusta University

library_source: genomic

data_processing:
Data was preprocessed with quality controls using FastQC, and then Bowtie2 aligned peaks.
After that, peaks were called with SEACR with the significance cut-off q-value <=0.01.
Peak annotation and mapping in relation to the proximal genes were performed using ChIP seeker. Finally, peaks were visualized by IGV.
Assembly: mm10
Supplementary files format and content: narrowPeak (except for IgG sample)
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Mouse CVGs

extract_protocol:
E11.5 CVGs were dissected and extracted nuclei immediately by incubating in the NE Buffer for 10 min on ice.
To prepare the library, 21ul DNA fragments was removed to PCR tube, to which 2 ul of barcoded i5 and i7 primers and 25 ul CUTANA High Fidelity 2x PCR Master Mix (EpiCypher, #15-1018) were added. PCR was performed using the following conditions: 72 °C for 5 min, 98 °C for 30 sec, and 20 (can be changed depending on experience with the sample) cycles of 98 °C for 10 sec, 63 °C for 10 sec, followed by an extra 1 min extension at 72 °C. The PCR product was analyzed on an Agilent Fragment Analyzer. Combined DNA libraries were cleaned up using AMPure XP beads (Beckman Coulter, #A63880) following the manufacturer’s instructions.

tag: age

value: Mouse CVGs

tag: cut&tag antibody


title: Day3_m4

description:
m03_4
male at day 3


title: Day3_f1

description:
f03_1
female at day 3


title: E11_5_CVG_H3K4me3_Rep1


title: MBT2#63_2

description:
S2
P+22/MBT2#63-20211029-01

value: Bladder cancer cell line


title: CHP-134 implanted in mice, RA-treated, RNA-seq Replicate 3 [CHP-134-L61]

city: Cordova

first: YINWEN

last: ZHANG

state: TN

address: 2189 Purple Leaf Ln

institute: stjude research hospital

data_processing:
The raw sequencing fastq files underwent quality and adapter trimming using trimgalore v0.4.4.
The trimmed reads were then mapped to the hg38 human reference genome using STAR v2.7.10a.
The abundance of transcripts and genes was estimated from the aligned reads using RSEM v1.3.3.
Assembly: hg38
Supplementary files format and content: gene_count, each column includes reads count of genes for each sample

source_name: xenograft tumor

extract_protocol:
Total RNA was extracted with TRIzol Reagent. For each sample, 150 ng of total RNA was used for library prep using Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus.
RNA-seq libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR). For each sample, 200 ng of RNA were mixed with 4 µl of diluted ERCC RNA Spike-In Mix. All libraries were sequenced on the Illumina NovaSeq 6000 system.

value: xenograft tumor

value: Neuroblastoma

value: 25mg/kg Oral gavage twice daily


title: CHP-134 implanted in mice, RA-treated, RNA-seq Replicate 4 [CHP-134-L72]


title: Day3_m3

description:
m03_3
male at day 3


title: Day3_f4

description:
f03_4
female at day 3


title: Day3_m2

description:
m03_2
male at day 3


title: MBT2#63_1

description:
S1
P+22/MBT2#63-20211029-01


title: E11_5_CVG_IgGM_Rep1

value: IgGM


title: LM8_1

description:
S3
P+7/LM8-20210524-01

value: Osteosarcoma cancer cell line


title: CHP-134 implanted in mice, RA-treated, RNA-seq Replicate 2 [CHP-134-L56]


title: TL-532_24H_#05

data_processing:
Base calling was realised using NCS 2.0.2 RTA 2.4.11
Demultiplexing was performed with Bcl2fastq  v2.17.1.14
trimming was realised with CutAdapt v1.9.1. Threshold quality score to 30  Minimum length of 50 bases after trimming.  The maximum rate of undetermined bases (“N”s) was set to 0%  Adapters were trimmed with 3 bases overlap, a maximum error rate of 10%
Reads mapping was realised with Kallisto v0.44.0
Normalisation and differential expression were performed using DEseq 2 R package v1.26.0
Assembly: Mus musculus – GRCm39
Ensembl - release 104
Supplementary files format and content: raw processed data  coming from Kallisto are under matrice format in .text
Supplementary files format and content: normalized count coming from DESeq are under matrix format in .text

source_name: bladder cancer cells MBT2

growth_protocol: We used the mouse model of syngeneic cell line MBT2 (bladder cancer), in the C3H/HeN mouse strain grafted ectopically and In treated by locoregional injection, mimicking the clinical administration of the drug candidate.

extract_protocol:
RNA extraction was performed with the RNeasy Fibrous tissue mini kit (Qiagen)
Library preparation : NEXTFLEX® Rapid Directional RNA-Seq Kit 2.0 (Perkin Elmer) with NEXTFLEX Poly(A) Beads 2.0 (Perkin Elmer)
Sequencing  : NextSeq 500, High output, Illumina, Single read 75nt

treatment_protocol: A treatment of 3 mg by intra-peritumoral injection and a subcutaneous peritumoral injection of 3 mg on the opposite side (i.e. 6 mg per treatment), were carried out on 12 mice bearing tumors of approximately 100 mm3.

value: bladder cancer cells MBT2

tag: syngeneic cell line


title: Day3_m1

description:
m03_1
male at day 3

value: kidney


title: CHP-134 implanted in mice, RA-treated, RNA-seq Replicate 1 [CHP-134-L54]


title: E11_5_CVG_IgGR_Rep3

value: IgGR


title: Day2_f4

description:
f02_4
female at day 2

value: wt

value: female


title: TL-532_24H_#13


title: E11_5_CVG_IgGR_Rep2


title: CHP-134 implanted in mice, untreated control, RNA-seq Replicate 5 [CHP-134-L73]

value: control


title: Day2_f3

description:
f02_3
female at day 2

value: cisplatin


title: TL-532_24H_#06


title: CHP-134 implanted in mice, untreated control, RNA-seq Replicate 4 [CHP-134-L60]


title: E11_5_CVG_IgGR_Rep1


title: E11_5_CVG_IgGM_Rep3


title: E11_5_CVG_IgGM_Rep2


title: Day2_f2

description:
f02_2
female at day 2


title: TL-532_6H_#14


title: CHP-134 implanted in mice, untreated control, RNA-seq Replicate 3 [CHP-134-L59]


title: Day2_m4

description:
m02_4
male at day 2


title: TL-532_6H_#08


title: E11_5_CVG_ISL1_70_Rep3


title: CHP-134 implanted in mice, untreated control, RNA-seq Replicate 1 [CHP-134-L49]


title: E11_5_CVG_POU4F1_Rep2


title: E11_5_CVG_POU4F1_Rep1


title: CHP-134 implanted in mice, untreated control, RNA-seq Replicate 2 [CHP-134-L55]


title: Day2_m3

description:
m02_3
male at day 2


title: TL-532_3H_#20


title: Day2_m2

description:
m02_2
male at day 2


title: CHP-134, 6day 2uM ATRA, RNA-seq Replicate2 [CHP-134-6d-2]

source_name: cell

value: cell

value: 6day 2uM ATRA


title: TL-532_3H_#02


title: CHP-134, 6day 2uM ATRA, RNA-seq Replicate1 [CHP-134-6d-1]


title: Day2_m1

description:
m02_1
male at day 2

value: male


title: E11_5_CVG_ISL1_70_Rep1

value: Mouse CVGs


title: Day0_f4

description:
f00_4
female at day 0


title: CHP-134, 3day 2uM ATRA, RNA-seq Replicate2 [CHP-134-3d-2]

value: 3day 2uM ATRA


title: E11_5_CVG_ISL1_26_Rep1


title: Mock_24H_#09


title: Day2_f1

description:
f02_1
female at day 2


title: Callus Macrophages-BulkRNAseq_Young16

city: Pittsburgh

first: Daniel

last: Clark

state: PA

address: 335 Sutherland Dr.

department: Periodontics and Preventive Dentistry

institute: University of Pittsburgh

data_processing:
scRNA-Seq
The R package Seurat (version 3.1.2) was used forsingle cell transcriptome analysis. The SCTransform normalization method was used to control for between-sample sequencing depth variation. Cells were removed according tothe following thresholds: <300 genes/cell or >3000 genes per cell, >20000 UMIs/cell, 5% mitochondrial content, <0.1% hemoglobin content. Among the cells retained, the effectsof mitochondrial content, ribosomal content, and sample/lanewere regressed out prior to clustering. Genes were excluded from the final datasetif they were expressed in fewer than 3cells, resulting in a total of 15,592genes.
Assembly: mm10
Supplementary files format and content: Comma seperated value text files for each sample include raw counts for each gene
RNA-Seq
Raw FASTQ sequencing reads were aligned using STAR_2.4.2a to the mouse genome (Ensemble Mouse GRCm38.78).
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: fracture callus

extract_protocol:
The fracture callus was isolated, dissociated with collagenase type 1, and a single cell suspension was created. Macrophages (CD45+, F4/80+, CD11b+) were isolated via flow cytometry (FACSAria). RNA was extracted using Invitrogen RNA aqueous Micro Kit (AM1931).
The library was prepared using Illumina TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Closed nonstable fractures were created in old (24mo) and young (3mo) mice. Animals were allowed to heal for three days

value: Macrophage

value: Young


title: TL-532_6H_#03


title: Day0_f3

description:
f00_3
female at day 0


title: Callus Macrophages-BulkRNAseq_Young15


title: Mock_6H_#01


title: CHP-134, 1day 2uM ATRA, RNA-seq Replicate2 [CHP-134-1d-2]

value: Neuroblastoma

value: 1day 2uM ATRA


title: Day0_f2

description:
f00_2
female at day 0


title: E11_5_CVG_ISL1_70_Rep2


title: Callus Macrophages-BulkRNAseq_Young14


title: Mock_3H_#11


title: CHP-134, 1day 2uM ATRA, RNA-seq Replicate1 [CHP-134-1d-1]


title: Day0_f1

description:
f00_1
female at day 0


title: CHP-134, DMSO, RNA-seq Replicate2 [CHP-134-0d-2]

value: DMSO


title: TL-532_3H_#10

value: bladder cancer cells MBT2


title: CHP-134, DMSO, RNA-seq Replicate1 [CHP-134-0d-1]


title: Callus Macrophages-BulkRNAseq_Young13


title: LP03011

city: Vienna

first: Hannes

last: Kühtreiber

state: Vienna

address: Lazarettgasse 14

department: Department of Dermatology

country: Austria

institute: Medical University Vienna

data_processing:
Illumina bcl2fastq command line tool (v2.19.1.403)
Reads in fastq format were generated using the Illumina bcl2fastq command line tool (v2.19.1.403), incl. trimming of the sequencing adapters.
Reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using STAR aligner version 2.6.1a in 2-pass mode.
Raw reads per gene were counted by STAR. Batch correction was performed using ComBat from sva version 3.35.2.
Assembly: Reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using STAR aligner version 2.6.1a in 2-pass mode
Supplementary files format and content: ProcessedDataMatrix.txt.gz contains a matrix with raw gene counts, gene symbols and gene types for each sample

source_name: gingiva

growth_protocol: Gingival fibroblasts were grown in Minimum Essential Medium Eagle (Sigma–Aldrich, St. Louis, MO, USA) supplemented with 10% fetal calf serum (Bio&Sell GmbH, Nuremberg, Germany) and 1% antibiotics (Sigma). The cells were seeded at 30,000 cells/cm2 onto culture dishes one day before being stimulated.

extract_protocol:
Total RNA was isolated utilizing the ExtractMe total RNA kit manufactured by Blirt S.A., Gdańsk, Poland.
Sequencing libraries were prepared at the Core Facility Genomics, Medical University of Vienna, using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina according to the manufacturer's protocols (New England Biolabs, Ipswich, MA) with unique dual indices (UDI). Libraries were QCchecked on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA H.S. Assay (Invitrogen, Waltham, MA).

treatment_protocol: Gingival fibroblasts were exposed to 30% PRF lysate and 10% PRF serum for 6 hours under standard conditions at 37 °C, 5% CO2, and 95% humidity.

value: gingiva

value: primary cells

value: gingival fibroblasts

value: wildtype

value: Platelet-rich fibrin (PRF) serum


title: CHP-134, 3day 2uM ATRA, RNA-seq Replicate1 [CHP-134-3d-1]


title: Day0_m4

description:
m00_4
male at day0

value: kidney

value: wt


title: LP03009

value: untreated


title: 786-O,TEAD_XMU,ChIP

city: Jinan

first: Tianwei

last: Jia

state: Shandong

address: 天桥区

institute: Shandong university

data_processing:
fastp software was used to remove the splicer sequence of the sequencing read segment
ChIP-Seq reads were aligned to the hg19 genome using Bowtie2 version2.4.5
narrowPeak files were generated using MACS2 callpeak with the significance cut-off q-value<=0.01.
bigWig files were generated using bedGraphToBigWig.
Getting the normalized bigwig file.
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

source_name: Clear cell renal

growth_protocol: RPMI-1640, 10% FBS, 1%penicillin/streptomycin. Cells were cultured at 37°C at 5% CO2

extract_protocol:
Cells were cross-linked by 1% warm formaldehyde for 10 min. After quenching and cell lysis, chromatin was sonicated using a water bath sonicator (Diagenode bioruptor).
We use 1x107 cells for one ChIP reaction. DNA was purified using the ChIP DNA Clean & Concentrator kit (D5205, Zymo Reasearch), and then subjected to Illumina ChIP-Seq library construction using VAHTS Universal Pro DNA Library Prep Kit (ND608,Vazyme).Post amplification libraries we're size selected at 300-700 bp in length using AMPure XP breads from Beckman Coulter. Libraries were validated using the Aglient 2100 Bioanalyzer.

value: Clear cell renal

value: carcinoma cell line


title: LP03010

value: Platelet-rich fibrin (PRF) membrane


title: Callus Macrophages-BulkRNAseq_Young12

value: Macrophage


title: Day0_m3

description:
m00_3
male at day0

value: male


title: Day0_m1

description:
m00_1
male at day0


title: Callus Macrophages-BulkRNAseq_Young10

value: Young


title: 786-O,Input_XMU,ChIP


title: LP03007


title: Callus Macrophages-BulkRNAseq_Young9


title: 786-O,p65_XMU,ChIP


title: LP03005


title: JAK1 siRNA + Th17 cells biol rep 3

city: Columbus

first: Gordon

middle: P

last: Meares

state: OH

address: 460 Medical Center Dr.

department: Neurology

institute: The Ohio State University

data_processing:
CLC Genomics Workbench 23
Sequences were trimmed for adaptor sequences and low quality reads (quality limit 0.05,
Trimmed sequences were mapped to Mus_musculus_sequence_mm10_o
Read counts and normalization were performed with CLC Genomics Workbench
Assembly: mm10
Supplementary files format and content: Tab demilited files including gene names, TPM, RPKM, and total gene counts

source_name: brain

growth_protocol: Mouse astrocytes cultured in DMEM with 10% FBS, antibiotics, non-essential amino acids, HEPES. Astrocytes were cultured for two weeks followed by removal of microglia by orbital shaking for 90 min. Astrocytes were then tyrpsinized and plated into 6 well plates.

extract_protocol:
Trizol followed by Dnase
Ribozero Plus + NEBNext Ultra II Directional

treatment_protocol: Forty-eight hours after plating, astrocytes were transfected using lipofectamine RNAiMax and siRNA silencer select non-targeting (control) or JAK1 siRNA. After 48 h, MOG-reactive Th17 cells were added to the astrocyte culture for 24 h. Isolation and polarization of T cells: Wild type female mice were immunized with MOG35-55 peptide emulsified in complete Freund's adjuvant. After 12 days, splenocytes and lymphocytes were isolated and cultured under Th17 polarizing conditions (IL-23, IL-6, IL-1beta, anti-IFN-gamma, and MOG peptide). After co-culture with astrocytes, T cells were removed by washing with PBS.

value: brain

value: neonatal astrocytes

value: JAK1 siRNA

value: Th17 co-culture


title: LP03006

value: gingiva

value: primary cells


title: JAK1 siRNA untreated biol rep 3


title: 786-O,Input_Veh,ChIP

value: vehicle


title: 786-O,p65_Veh,ChIP


title: Callus Macrophages-BulkRNAseq_Young7


title: Callus Macrophages-BulkRNAseq_Young11


title: LP03002

value: gingival fibroblasts

value: wildtype


title: control siRNA + Th17 cells biol rep 3

value: control siRNA


title: 786-O,p65_siTEAD4,ChIP

value: siTEAD


title: Day0_m2

description:
m00_2
male at day0

value: kidney

value: wt


title: Callus Macrophages-BulkRNAseq_Young6


title: Callus Macrophages-BulkRNAseq_Old15

value: Old


title: LP03001

value: untreated


title: JAK1 siRNA + Th17 cells biol rep 2


title: Callus Macrophages-BulkRNAseq_Young8

value: Macrophage


title: Callus Macrophages-BulkRNAseq_Old14


title: SW480_spheres_rep4

city: Rotterdam

first: Mathijs

last: Verhagen

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

data_processing:
Illumina paired-end reads of 76 bp were trimmed by removing the TrueSeq adapter sequences using Trimmomatic (v.0.33).
Reads were mapped to the human reference genome build hg38 with the RNA-seq aligner STAR (v2.4.2a) and the Homo sapiens GENCODE v23 annotation.
Raw counts were summed with featureCounts (v2.0.3)
Downstream analysis was done in R with DESeq2 (1.36.0).
Counts were normalized with a variance stabilizing transformation (VST).
Assembly: hg38
Supplementary files format and content: Excel file includes Ensemble Gene Ids and variance stabilizing transformation (VST) normalized counts.

source_name: colon

growth_protocol: SW480 subpopulations were sorted and grown in standard culture medium for 4 days before RNA was extracted.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA-Seq was performed at the Erasmus MC Center for Biomics (Rotterdam, The Netherlands) according to manufacturer’s instructions (Illumina) and using the TruSeq RNA sample prep kit v2. Briefly, polyA containing mRNA molecules were purified using poly-T oligo attached magnetic beads. Following purification, the mRNA was fragmented into ~200 bp fragments using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand synthesis using DNA polymerase I and RNaseH treatment. These cDNA fragments were end repaired, a single A base was added and Illumina adapters were ligated. The products were purified and size selected on gel and enriched by PCR. The PCR products were purified by Qiaquick PCR purification and used for cluster generation according to the Illumina cluster generation protocols.

treatment_protocol: no treatment was applied

value: colon

value: grade 3-4 colon adenocarcinoma

tag: subpopulation

value: sphere subpopulation


title: LP03003

value: Platelet-rich fibrin (PRF) serum


title: 786-O,Input_Ctrl,ChIP

value: Clear cell renal

value: carcinoma cell line


title: control siRNA untreated biol rep 3

value: brain

value: neonatal astrocytes


title: SW480_spheres_rep2


title: control siRNA + Th17 cells biol rep 2

value: Th17 co-culture


title: SW480_spheres_rep3


title: 786-O,p65_Ctrl,ChIP


title: Callus Macrophages-BulkRNAseq_Old12


title: Callus Macrophages-BulkRNAseq_Old13


title: control siRNA untreated biol rep 2


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-22 d60 lymph node bio rep 2

city: St. Louis

first: Julian

last: Zhou

state: MO

address: 425 S. Euclid Ave.

department: Pathology & Immunology

institute: Washington University in St. Louis

description: 10x Genomics

data_processing:
Sequences were processed using Cell Ranger software version 6.1.2
Assembly: GRCh38
Supplementary files format and content: Each matrix.mtx.gz contains a gene expression count matrix stored in the Market Exchange Format for sparse matrices
Supplementary files format and content: Each features.tsv.gz contains feature information that corresponds to the row indices of matrix.mtx.gz
Supplementary files format and content: Each barcodes.tsv.gz contains cellular barcodes that correspond to the column indices of matrix.mtx.gz
Supplementary files format and content: Each filtered_contig_annotations.csv contains processed and annotated T cell receptors

source_name: Lymph Node

extract_protocol:
Frozen PBMC samples were thawed, washed once with R10, and then washed with P2. PBMC were counted on a Cellometer Auto 2000 (Nexcelom) and resuspended to a final concentration of approximately 108 cells/mL in P2. Total untouched CD3+ or positively selected CD4+ T cells were enriched using either the EasySep Human T Cell Isolation Kit or the EasySep Human CD4 positive selection kit II, respectively, with the EasyEights magnet (STEMCELL Technologies) all per the manufacturer’s instructions. Following enrichment, T cell populations were washed with P2, re-counted and resuspended in PBS supplemented with 0.05% BSA.
Chromium single cell 5’ v2 gene expression and Chromium single cell V(D)J libraries (10x Genomics) were prepared according to the manufacturer’s instructions without modifications.

value: Lymph Node


title: SW480_spheres_rep1


title: Callus Macrophages-BulkRNAseq_Old11


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-22 d60 lymph node bio rep 1

description: 10x Genomics


title: JAK1 siRNA + Th17 cells biol rep 1

value: JAK1 siRNA


title: SW480_bulk_rep4

value: bulk subpopulation


title: SW480_bulk_rep3


title: Callus Macrophages-BulkRNAseq_Old10


title: JAK1 siRNA untreated biol rep 2


title: Callus Macrophages-BulkRNAseq_Old9


title: JAK1 siRNA untreated biol rep 1


title: SW480_bulk_rep2


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-22 d201 peripheral blood bio rep 2

description: 10x Genomics

source_name: Peripheral Blood

value: Peripheral Blood


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-22 d201 peripheral blood bio rep 1

description: 10x Genomics


title: control siRNA + Th17 cells biol rep 1

value: control siRNA


title: Callus Macrophages-BulkRNAseq_Old8

value: Old


title: control siRNA untreated biol rep 1


title: 786-O,Input_siTEAD4,ChIP

value: siTEAD


title: Callus Macrophages-BulkRNAseq_Old6

value: Macrophage


title: ILC3s, ko_4

first: Siyan

last: Cao

address: 660 S Euclid Ave

department: Gastroenterology

data_processing:
cDNA was then fragmented and blunt ended. A base was added to 3′ ends of cDNA fragments, and Illumina sequencing adapters were ligated to the ends. Ligated fragments were then amplified and sequenced (Illumina HiSeq). After basecalling and demultiplexing, RNA-seq reads were aligned to mm10 genome. Aligned gene counts were processed using DESeq2 package (67) with R (version 4.3.2). Genes with fewer than 10 counts among all samples were excluded. For DEG analysis, only protein-coding genes with an average expression of > 100 counts per sample were used. The threshold of DEG was set as “adjusted p value” < 0.05 and |log2FoldChange| > 1. GSEA analysis was performed using clusterProfiler package (68) with R. Genes for GSEA analysis were filtered as protein-coding genes with an average expression > 100 counts and “adjusted p value” < 0.1.
Assembly: mm10
Supplementary files format and content: all.gene_counts.tsv

source_name: intestine

extract_protocol:
Total RNA was extracted by QIAGEN Rneasy Plus Micro Kit.
cDNA was prepared using SMARTer Ultra Low RNA kit for Illumina Sequencing

value: intestine

value: colitis


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-22 d110 peripheral blood bio rep 1

description: 10x Genomics


title: ILC3s, ko_3


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-22 d110 lymph node bio rep 2

description: 10x Genomics


title: HCC1395_KD_3

city: Miami

first: Karoline

middle: J

last: Briegel

state: Florida

address: 1600 NW 10th Avenue

department: Surgery

institute: University of Miami Miller School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR (ver.2.5.0).
The mapped data were assigned with genomic features with featureCounts ver.1.5.0 (Liao, et al., 2014).
Fold changes of differential expression between two conditions per cell line (two or three biological replicates per group) were estimated through edgeR ( Robinson, et al., 2014) with exact Test.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Cell Line

growth_protocol: BT549, MDA-MB-231 were grown in DMEM+10% FBS, Non-essential Amino Acids and Pen-Strep; HCC1395 in RPMI+10% FBS, Pen-Strep;  and MCF7 in IMEM+10%FBS, Insulin and Pen-Strep in a 5% CO2 incubator at 37°C. Mycoplasma tests were routinely performed using MycoAlert Mycoplasma Detection Kit (Lonza).

extract_protocol:
Total RNA was harvested from cell samples using TriZol reagent (Invitrogen). Illumina TruSeq RNA Sample Prep Kit used 1 ug of total RNA starting material for mRNA enrichement followed by construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEB RNA-Seq NSG library prep kit.

treatment_protocol: Stable LBH-overexpressing BT549 cell lines were generated by nucleofection of linearized pCDNA3 vector or pCDNA3+Lbh expression plasmids in Solution V (Lonza). MCF7 cells were stably transfected with pCDNA3 or pCDNA3+Lbh DNA plasmids using Lipofectamine 2000. For LBH knockdown  in HCC1395 and MDA-MB-231, triplicate samples of cells were transiently transfected with 2 nM of synthetic siRNA specific for LBH or a scrambled control sequence (Dharmacon SmartPool) using Dharmafect #1 transfection reagent according to manufacturer’s protocol.  Cells were grown in siRNA containing media at 37°C, 5% CO2 for 72 hours prior to analysis.

value: breast cancer

value: LBH Knock Down


title: HCC1395_KD_2


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-22 d110 lymph node bio rep 1

description: 10x Genomics


title: ILC3s, ko_2


title: HCC1395_KD_1


title: dna2_aid H3K56ac_eSPAN 25C 30' MNase, IAA1 rep1 [Alb726_dna2_aid_H3K56ac_eSPAN_S]

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
Raw reads were firstly trimmed by Cutadapt (Marcel, 2011) to remove adapters and low quality reads, and then mapped to the yeast genome (sacCer3) using Bowtie2 (Langmead and Salzberg, 2012).Duplicate reads were further filtered by Sambamba (Tarasov et al., 2015) to remove PCR duplication.
The genome-wide read coverage on Watson and Crick strands were calculated at the bin of 1bp using deepTools bamCoverage (Ramirez et al., 2016). Then, the raw genome-wide read coverage was normalized with the number of total mapped reads to obtain counts per million value (CPM).
Spike-in added samples normalization. For each Sonication-BrdU-IP-ssSeq sample, the raw genome-wide coverage was normalized using the formula: BrdUsoni = (BrdUcov / BrdUspike) / (Inputread / Inputspike). BrdUcov is the raw coverage of BrdU-IP-ssSeq; BrdUspike is the number of total mapped spike-in reads (S. pombe reads) in BrdU sample, Inputread is the number of total mapped reads in input, and Inputspike is the number of total mapped spike-in reads (S. pombe) in input. In this way, BrdU incorporation at each strain was quantified as BrdUsoni.
Spike in added samples normalization. For each MNase-BrdU-IP-ssSeq dataset, reads with the nucleosome sized (120~170bp) were first selected to calculate the raw coverage of nucleosome occupancy surrounding replication origins, and then normalized using the formula: BrdUMNase = (BrdUcov-MNase / BrdUspike-MNase) / (Inputread-MNase / Inputspike-MNase). BrdUcov-MNase is the raw coverage of the nucleosome-sized reads, BrdUspike-MNase is the number of mapped nucleosome-sized spike-in reads in the same sample, Inputread-MNase is the number of mapped  nucleosome-sized reads in input, and Inputspike-MNase is the number of mapped nucleosome-sized spike-in reads in the same input sample. In this way, the nucleosome occupancy on nascent chromatin was quantified as BrdUMNase.
Assembly: saccer3
Supplementary files format and content: tar of bw, bigwig format, CPM which is normalized by total number of reads
Supplementary files format and content: tar of bw, bigwig format, BrdU coverage normalized by spike-in and input described as formulas above.

organism: Saccharomyces cerevisiae

growth_protocol: For most experiments, yeast cells were cultured and synchronized at G1 phase following standard procedures (Dunham et al., 2015). ChIP, BrdU-IP-ssSeq, and eSPAN sample collection was performed as described previously (Gan et al., 2017; Yu et al., 2018). Briefly, exponentially growing yeast cultures at OD600=0.4-0.5 were synchronized by adding a-factor at 5mg/ml and arrested for 3h at 25°C.

extract_protocol:
For analysis of DNA replication by BrdU-IP-ssSeq, and PCNA ChIP and eSPAN experiments, chromatin was fragmented by sonication (15 seconds on and 30 seconds off for 10 cycles in a Bioruptor Pico, Diagenode). For analysis of nucleosome occupancy at nascent chromatin, H3K4me3 and H3K56ac ChIP as well as almost all eSPAN experiments except those marked by sonication, chromatin was digested with MNase to map nucleosomes (Wal and Pugh, 2012).
The ssDNA libraries were prepared using the Accel-NGS 1S Plus kit (Cat no. 10096, Swift Bioscience).

treatment_protocol: Cells were then released into fresh YPD medium containing 400mg/ml BrdU without HU for 30 or 40 minutes at 25°C. For experiments using auxin-inducible protein degradation mutant strains, 1mM IAA or the equivalent volume of ethanol was added to the arresting culture (30 minutes before release) and cells were released in YPD medium also containing IAA or ethanol.

tag: batch

tag: condition

value: 25C 30' MNase, IAA1


title: dna2_aid H3K4me3_eSPAN 25C 30' MNase, IAA1 rep1 [Alb725_dna2_aid_H3K4me3_eSPAN_S]


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-20 d60 lymph node bio rep 2

description: 10x Genomics


title: HCC1395_NT_3

value: Non Target siRNA Control


title: ILC3s, ko_1


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-20 d60 lymph node bio rep 1

description: 10x Genomics


title: ILC3s, ctr_5


title: HCC1395_NT_2


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-22 d110 peripheral blood bio rep 2

description: 10x Genomics


title: SW480_bulk_rep1

value: colon

value: grade 3-4 colon adenocarcinoma


title: ILC3s, ctr_3


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-20 d201 lymph node bio rep 2

description: 10x Genomics


title: Callus Macrophages-BulkRNAseq_Old7


title: dna2AID+IAA H3K56ac_eSPAN 25C 30' MNase, IAA1 rep1 [Alb966_dna2AIDpIAA_H3K56ac_eSPAN_S30]


title: HCC1395_NT_1


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-20 d201 lymph node bio rep 1

description: 10x Genomics


title: ILC3s, ctr_2


title: dna2AID+IAA H3K4me3_eSPAN 25C 30' MNase, IAA1 rep1 [Alb965_dna2AIDpIAA_H3K4me3_eSPAN_S30]


title: dna2AID+IAA BrdU 25C 30' MNase, IAA1 rep1 [Alb964_dna2AIDpIAA_BrdU_S30]

source_name: dna2AID+IAA BrdU 25C 30' MNase, IAA1

value: BrdU


title: MDA-MB231_KD_2


title: dpb3pol3079 H3K56ac_eSPAN 25C 30' sonication rep1 [Alb742_dpb3pol3079_H3K56ac_eSPAN_S]

value: 25C 30' sonication


title: MDA-MB231_KD_3


title: ILC3s, ctr_1


title: MDA-MB231_KD_1


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-20 d110 lymph node bio rep 1

description: 10x Genomics

value: Lymph Node


title: dpb3pol3079 H3K4me3_eSPAN 25C 30' sonication rep1 [Alb741_dpb3pol3079_H3K4me3_eSPAN_S]


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-20 d110 lymph node bio rep 2

description: 10x Genomics


title: ATAC mouse HSPCs

city: Beijing

first: Xun

last: Lan

address: Haidian District

department: School of Medicine

institute: Tsinghua University

data_processing:
For Tracking-seq, please refer to https://github.com/Lan-lab/offtracker.
For other data, fastq files were mapped to mm10 using bowtie2. SAM files were converted to BAM files with samtools. BAM files were converted to bedgraph files by deeptools and then converted to bigwig files with bedGraphToBigWig after normalization
Assembly: hg38 or mm10
Supplementary files format and content: BigWig of sequencing signals

source_name: mHSPC

extract_protocol:
100,000 NIH3T3 cells, AML12 cells, mHSPCs, or mESCs were sorted into tube for tagmentation and purifcation.
Tagged DNA were PCR amplified with primers containing barcodes to construct the sequencing libraries.
For Tracking-seq, cells were fixed with Concanavalin A bead, washed, and resuspended with buffer containing RPA2/IgG antibodies. pA-MNase was added to cleavage the DNA. Cleavaged fragments were collected and then digested with DNase. For Tracking-seq, DNA was purified with DNA Clean Beads and then HL-dsDNase was added to remove dsDNA.  For ChIP-seq, Cells were crosslinked with 1% formaldehyde. After quenching and blocking the beads, MRE11 or H3K4me3 antibody were added. After cell lysis, the lysate was sonicated using a QSONICA sonicator with microtips. DNA was then treated with RNase A and Proteinase K, followed by purification through phenol-chloroform extraction. For ATAC-seq, 100,000 NIH3T3 cells, AML12 cells, mHSPCs, or mESCs were sorted into tube for tagmentation and purifcation.
The strand-specific ssDNA libraries were constructed using VAHTS ssDNA Library Prep Kit. Other libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit.

value: mHSPC


title: ATAC NIH3T3 cells


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-16 d28 lymph node 2 bio rep 2

description: 10x Genomics


title: MDA-MB231_NT3


title: dpb3pol3079 BrdU 25C 30' sonication rep1 [Alb740_dpb3pol3079_BrdU_S]

source_name: dpb3pol3079 BrdU 25C 30' sonication


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-16 d28 lymph node 2 bio rep 1

description: 10x Genomics


title: ATAC mouse ESCs

source_name: mESC

value: mESC


title: dna2_aid BrdU 25C 30' MNase, IAA1 rep1 [Alb724_dna2_aid_BrdU_S]

source_name: dna2_aid BrdU 25C 30' MNase, IAA1


title: MDA-MB231_NT_2


title: ATAC AML12 cells


title: MDA-MB231_NT_1


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-16 d28 lymph node 1 bio rep 1

description: 10x Genomics


title: H3K4me3 NIH3T3 cells

extract_protocol:
Cells were crosslinked with 1% formaldehyde. After quenching and blocking the beads, MRE11 or H3K4me3 antibody were added. After cell lysis, the lysate was sonicated using a QSONICA sonicator with microtips. DNA was then treated with RNase A and Proteinase K, followed by purification through phenol-chloroform extraction.
The libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit.
For Tracking-seq, cells were fixed with Concanavalin A bead, washed, and resuspended with buffer containing RPA2/IgG antibodies. pA-MNase was added to cleavage the DNA. Cleavaged fragments were collected and then digested with DNase. For Tracking-seq, DNA was purified with DNA Clean Beads and then HL-dsDNase was added to remove dsDNA.  For ChIP-seq, Cells were crosslinked with 1% formaldehyde. After quenching and blocking the beads, MRE11 or H3K4me3 antibody were added. After cell lysis, the lysate was sonicated using a QSONICA sonicator with microtips. DNA was then treated with RNase A and Proteinase K, followed by purification through phenol-chloroform extraction. For ATAC-seq, 100,000 NIH3T3 cells, AML12 cells, mHSPCs, or mESCs were sorted into tube for tagmentation and purifcation.
The strand-specific ssDNA libraries were constructed using VAHTS ssDNA Library Prep Kit. Other libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit.


title: dpb3pol3079 H3K4me3_eSPAN 25C 30' MNase rep1 [Alb733_dpb3pol3079_H3K4me3_eSPAN_S]

source_name: dpb3pol3079 H3K4me3_eSPAN 25C 30' MNase

value: 25C 30' MNase


title: MCF7_OE_3

value: LBH Over Expression


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-16 d201 lymph node 2 bio rep 2

description: 10x Genomics


title: H3K4me3 AML12 cells


title: dpb3pol3079 H3K56ac_eSPAN 25C 30' MNase rep1 [Alb734_dpb3pol3079_H3K56ac_eSPAN_S]

source_name: dpb3pol3079 H3K56ac_eSPAN 25C 30' MNase


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-16 d28 lymph node 1 bio rep 2

description: 10x Genomics


title: MCF7_OE_2


title: elg14A PCNA_eSPAN 25C 30' sonication rep1 [Alb806_elg14A_PCNA_eSPAN_S30]

source_name: elg14A PCNA_eSPAN 25C 30' sonication


title: WT mHSPC 100k rep1

data_processing:
For Tracking-seq, please refer to https://github.com/Lan-lab/offtracker.
For other data, fastq files were mapped to mm10 using bowtie2. SAM files were converted to BAM files with samtools. BAM files were converted to bedgraph files by deeptools and then converted to bigwig files with bedGraphToBigWig after normalization
Assembly: hg38 or mm10
Supplementary files format and content: BigWig of sequencing signals
Library strategy: Track-seq

extract_protocol:
Cells were fixed with Concanavalin A bead, washed, and resuspended with buffer containing RPA2/MRE11/IgG antibodies. pA-MNase was added to cleavage the DNA. Cleavaged fragments were collected and then digested with DNase. For Tracking-seq, DNA was purified with DNA Clean Beads and then HL-dsDNase was added to remove dsDNA.
The strand-specific ssDNA libraries were constructed using VAHTS ssDNA Library Prep Kit. CUT&RUN-MRE11 library was constructed using NEBNext® Ultra™ II DNA Library Prep Kit.
For Tracking-seq, cells were fixed with Concanavalin A bead, washed, and resuspended with buffer containing RPA2/IgG antibodies. pA-MNase was added to cleavage the DNA. Cleavaged fragments were collected and then digested with DNase. For Tracking-seq, DNA was purified with DNA Clean Beads and then HL-dsDNase was added to remove dsDNA.  For ChIP-seq, Cells were crosslinked with 1% formaldehyde. After quenching and blocking the beads, MRE11 or H3K4me3 antibody were added. After cell lysis, the lysate was sonicated using a QSONICA sonicator with microtips. DNA was then treated with RNase A and Proteinase K, followed by purification through phenol-chloroform extraction. For ATAC-seq, 100,000 NIH3T3 cells, AML12 cells, mHSPCs, or mESCs were sorted into tube for tagmentation and purifcation.
The strand-specific ssDNA libraries were constructed using VAHTS ssDNA Library Prep Kit. Other libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit.


title: MCF7_OE_1


title: WT mESC 200k rep1


title: elg14A PCNA_ChIP 25C 30' sonication rep1 [Alb804_elg14A_PCNA_ChIP_S30]

source_name: elg14A PCNA_ChIP 25C 30' sonication


title: MCF7_Vec_3

value: Vector Control


title: WT liver 500k rep1

source_name: Liver

value: Liver


title: elg14A BrdU 25C 30' sonication rep1 [Alb805_elg14A_BrdU_S30]

source_name: elg14A BrdU 25C 30' sonication


title: MCF7_Vec_2


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-16 d201 lymph node 1 bio rep 1

description: 10x Genomics


title: elg1D PCNA_eSPAN 25C 40' sonication rep2 [Alb667_elg1D_PCNA_eSPAN_S40]

source_name: elg1D PCNA_eSPAN 25C 40' sonication

value: 25C 40' sonication


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-13 d60 lymph node bio rep 2

description: 10x Genomics


title: MCF7_Vec_1


title: elg1D PCNA_eSPAN 25C 40' sonication rep1 [Alb594_elg1D_PCNA_eSPAN_S40]


title: dpb3pol3079 BrdU 25C 30' MNase rep1 [Alb732_dpb3pol3079_BrdU_S]

source_name: dpb3pol3079 BrdU 25C 30' MNase


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-13 d60 lymph node bio rep 1

description: 10x Genomics

source_name: Lymph Node


title: BT549_OE_3


title: WT NIH3T3 200k rep1


title: Cas9 Pcsk9 96h liver 250k rep1


title: BT549_OE_2


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-13 d201 peripheral blood bio rep 2

description: 10x Genomics

source_name: Peripheral Blood

value: Peripheral Blood


title: elg1D PCNA_ChIP 25C 40' sonication rep2 [Alb665_elg1D_PCNA_ChIP_S40]

source_name: elg1D PCNA_ChIP 25C 40' sonication


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-16 d201 lymph node 1 bio rep 2

description: 10x Genomics


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-16 d201 lymph node 2 bio rep 1

description: 10x Genomics


title: BT549_OE_1

source_name: Cell Line

value: breast cancer


title: Cas9 Pcsk9 48h mHSPC 150k rep1


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-13 d201 peripheral blood bio rep 1

description: 10x Genomics


title: Cas9 Pcsk9 48h Neuron 100k rep2

source_name: Neuron

value: Neuron


title: BT549_Vec_3


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-13 d110 peripheral blood bio rep 2

description: 10x Genomics


title: elg1D BrdU 25C 40' sonication rep2 [Alb666_elg1D_BrdU_S40]

source_name: elg1D BrdU 25C 40' sonication


title: WT Neuron 100k rep1


title: BT549_Vec_2


title: elg1D BrdU 25C 40' sonication rep1 [Alb593_elg1D_BrdU_S40]


title: elg1D PCNA_eSPAN 25C 30' sonication rep2 [Alb663_elg1D_PCNA_eSPAN_S30]

source_name: elg1D PCNA_eSPAN 25C 30' sonication


title: elg1D PCNA_ChIP 25C 40' sonication rep1 [Alb592_elg1D_PCNA_ChIP_S40]


title: Cas9 Pcsk9 24h mHSPC 60k rep1

source_name: mHSPC


title: BT549_Vec_1


title: elg1D PCNA_eSPAN 25C 30' sonication rep1 [Alb590_elg1D_PCNA_eSPAN_S30]


title: CVG, DKO, E11.5

data_processing:
The Trimmomatic software was used to filter and trim minority low quality sequencing reads from the data set.
The quality of sequence reads in the FASTQ files was evaluated using the FastQC analysis.
High quality sequence reads were aligned to the mouse mm10 reference transcriptome using the HISAT2. The HISAT2 outputs were transformed with SAMtools and then fed into StringTie for transcript quantification.
the count tables or matrices were input into the LEPSeq statistical package for determination of differential transcript expression between samples (cutoff fold change ≥ 2 and P value ≤ 0.05).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM and TPM values for each Sample

source_name: CVG neurons

extract_protocol:
Total RNA was extracted from fresh frozen tissue using Trizol following manufacturer’s instructions (ThermoFisher Scientific, Waltham, MA, USA).
Strand-specific RNA sequencing library was prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: CVGs were dissected out and froze in liquid nitrogen immediately.

value: CVG neurons

value: DKO

value: Embyronic 11.5


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-04 d60 lymph node bio rep 2

description: 10x Genomics


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-04 d60 lymph node bio rep 1

description: 10x Genomics


title: elg1D PCNA_ChIP 25C 30' sonication rep2 [Alb661_elg1D_PCNA_ChIP_S30]

source_name: elg1D PCNA_ChIP 25C 30' sonication


title: Cas9 Pcsk9 24h NIH3T3 200k rep1


title: Cas9 Pcsk9 24h mESC 30k rep1

source_name: mESC


title: CVG, Isl1CKO, E11.5


title: Cas9 Pcsk9 24h AML12 100k rep1


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-04 d28 lymph node bio rep 2

description: 10x Genomics


title: CVG, Pou4f1KO, E11.5


title: elg1D PCNA_ChIP 25C 30' sonication rep1 [Alb588_elg1D_PCNA_ChIP_S30]


title: elg1D BrdU 25C 30' sonication rep2 [Alb662_elg1D_BrdU_S30]

source_name: elg1D BrdU 25C 30' sonication


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-04 d28 lymph node bio rep 1

description: 10x Genomics


title: Cas9 Pcsk9 48h Neuron 100k rep1


title: Cas9 Pcsk9 24h NIH3T3 100k rep1


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-13 d110 lymph node bio rep 1

description: 10x Genomics


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-04 d201 peripheral blood bio rep 2

description: 10x Genomics


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-13 d110 peripheral blood bio rep 1

description: 10x Genomics


title: CVG, control, E11.5

value: control


title: Pancreas from Pdx1-Cre+, poh1f/f mice rep2

city: Shanghai

first: Boshi

address: No.800 Dongchuan Road

institute: Shanghai Cancer Institute

data_processing:
The row RNA-seq data were qualified by FastQC (0.11.9) and then trimmed by trim_galore (0.6.6).
SortMeRNA (4.2.0) was used to remove rRNA reads to generate clean data.
The clean reads were aligned to the mouse reference genome (GRCm38) using STAR (2.7.6a) aligner to generate BAM files.
Samtools (1.7) software was used to remove duplicates. The unique mapped counts were determined by featureCounts (2.0.1).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include unique mapped counts

source_name: Pancreas

extract_protocol:
Total RNA was extracted by TRIzol Reagent (Life Technologies, CA, USA) according to the manufacturer’s instructions, and RIN values were measured using an Agilent Bioanalyzer 2100 (Agilent Technologies, CA, USA) to inspect RNA integrity.
Qualified total RNA was further purified using an RNAClean XP Kit (Beckman Coulter, Inc. CA, USA) and RNase-Free DNase Set (QIAGEN, GmBH, Germany). RNA libraries were prepared for sequencing using a VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, Nanjing, China).

value: Pancreas

value: tissue

value: pancreatic cells

value: Pdx1-Cre+, poh1f/f


title: elg1D BrdU 25C 30' sonication rep1 [Alb589_elg1D_BrdU_S30]

value: 25C 30' sonication

value: BrdU


title: In_vitro_Multiome_ATAC_IL4

city: New Haven

first: Rong

last: Fan

state: Connecticut

address: 55 Prospect St.

department: Biomedical Engineering

institute: Yale University

description:
atac_fragments.tsv.gz.tbi
atac_peak_annotation.tsv
filtered_feature_bc_matrix.h5
atac_fragments.tsv.gz

library_source: genomic single cell

data_processing:
For scRNA-seq, the raw fastq files were generated and demultiplexed by CeleScope rna from Singleron (version 3.0.1) and primary data analysis was performed with CeleScope (version 1.10.0) using a custom reference package based on reference genome (Mus_musculus_ensembl_92)
For ATAC+Gene multiomics, the Cell Ranger ARC v2.0.2 (10x Genomics) was utilized to perform sample demultiplexing, barcode processing, identification of open chromatin regions, and simultaneous counting of transcripts and peak accessibility in single cells from the sequenced data.
Assembly: Mus_musculus_ensembl_92
Supplementary files format and content: Gene expression matrix
Supplementary files format and content: Combined Gene+ATAC expression matrix and ATAC fragments and annotation files

source_name: Spleen

growth_protocol: Tumors were collected and digested, and tumor-infiltrating PMEL T cells were enriched and sorted out for scRNA-seq

extract_protocol:
In vivo scRNA-seq was performed using the GEXSCOPE Single Cell RNA Library Kit Cell V2 reagents (Singleron Biotechnologies GmbH). In vitro single-cell ATAC+gene multiome was performed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics, Cat# PN-1000283)
Libraries were constructed according to the protocols provided by the aforementioned kits.
scRNA-seq and single cell ATAC+Gene multiomics

value: Spleen

value: T cells


title: In_vitro_Multiome_ATAC_PBS

value: PBS


title: Pancreas from Pdx1-Cre+, poh1f/+ mice rep2

value: Pdx1-Cre+, poh1f/+


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d60 lymph node bio rep 2

description: 10x Genomics

value: Lymph Node


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-04 d110 peripheral blood bio rep 1

description: 10x Genomics

value: Peripheral Blood


title: Callus Immune cells-scRNAseq_YoungA

source_name: fracture callus

extract_protocol:
The fracture callus was isolated, dissociated with collagenase type 1, and a single cell suspension was created. Immune cells (CD45+) were isolated via flow cytometry (FACSAria).
The library was prepared from a single cell suspension. Library preparation was performed using the Chromium Single Cell 3’ Reagent Version 2 Kit by 10X Genomics. Cells from each sample were loaded into their respective 10X chip wells. Libraries were prepared according to 10X Genomics guidelines and sequenced on an Illumina HiSeq2500.

value: Immune cells (CD45+)

value: Young


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d28 lymph node bio rep 2

description: 10x Genomics


title: Callus Immune cells-scRNAseq_OldB

value: Old


title: pol306 PCNA_eSPAN 25C 30' sonication rep2 [Alb692_merge_pol306_PCNA_eSPAN]

source_name: pol306 PCNA_eSPAN 25C 30' sonication


title: Callus Immune cells-scRNAseq_OldA


title: Pancreas from Pdx1-Cre+, poh1f/f mice rep1


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-04 d201 peripheral blood bio rep 1

description: 10x Genomics


title: elg1D H3K56ac_eSPAN 25C 30' MNase rep2 [Alb884_elg1D_H3K56ac_eSPAN_S30]

source_name: elg1D H3K56ac_eSPAN 25C 30' MNase

value: 25C 30' MNase


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d201 peripheral blood bio rep 2

description: 10x Genomics


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d201 peripheral blood bio rep 1

description: 10x Genomics


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-04 d110 peripheral blood bio rep 2

description: 10x Genomics


title: elg1D H3K56ac_eSPAN 25C 30' MNase rep1 [Alb194_elg1_H3K56ac_eSPAN_S30]


title: pol306 PCNA_ChIP 25C 30' sonication rep1 [Alb604_pol306_PCNA_ChIP_S30]

source_name: pol306 PCNA_ChIP 25C 30' sonication


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d60 lymph node bio rep 1

description: 10x Genomics

source_name: Lymph Node


title: In_vitro_Multiome_Gene_IL4

molecule: nuclear RNA


title: Acacetin 4

city: Urumqi

first: juan

last: Bu

address: 29 Tianchi Road

institute: People's Hospital of Xinjiang Uygur Autonomous Region

data_processing:
Illumina bcl2fastq software used for basecalling.
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
The dataset containing the clean reads was aligned to the GCRm39 genome by HISAT2 allowing 4 mismatches.
Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped)
DEGs were screened out using the R Bioconductor package DESeq2.The P value <0.05 and fold change>1.5 or < 0.67 were set as the cut-off criteria for identifying DEGs.
Assembly: GRCm39
Supplementary files format and content: reads counts, FPKM for each Sample

source_name: BV2 cells

extract_protocol:
Total RNAs were extracted from BV2 cells using TRIzol Reagent (Invitrogen, cat. NO 15596026.DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with Nanodrop OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qubit3.0 was used to quantify qualified RNAs using the QubitTM RNA Broad Range Assay kit(Life Technologies, Q10210).
A total of 2ug RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China). PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: BV2 cells

value: Acacetin


title: elg1D H3K4me3_eSPAN 25C 30' MNase rep1 [Alb193_elg1_H3K4me3_eSPAN_S30]

source_name: elg1D H3K4me3_eSPAN 25C 30' MNase


title: elg1D H3K4me3_eSPAN 25C 30' MNase rep2 [Alb883_elg1D_H3K4me3_eSPAN_S30]


title: Callus Immune cells-scRNAseq_YoungB


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d201 lymph node bio rep 1

description: 10x Genomics


title: pol306 BrdU 25C 30' sonication rep2 [Alb652_pol306_BrdU_S30]

source_name: pol306 BrdU 25C 30' sonication


title: HU-231024_delta.Hif2a

city: Erlangen

first: Pang

last: Lyu

address: Glückstr. 6

department: Department of Internal Medicine 3

country: Germany

institute: University Hospital Erlangen

data_processing:
RNA was isolated from the small intestine epithelial cells of Hif2α flox/flox Villin-cre+ mice and their WT littermates.
For each sample a DNA fragment library is generated using the Illumina TruSeq Stranded mRNA kit. The libraries are sequenced single end with 101 bp length on an Illumina HiSeq 2500 platform. TruSeq sequencing adapter sequences are trimmed from the reads and trimmed reads shorter than 60 bp are discarded (cutadapt v1.18). Read quality is checked after sequencing and after base trimming. (fastqc v0.11.8).
The processed reads are mapped to the mouse reference genome GRCm38 with the GENCODE annotation M23 (equals Ensembl 98) using the splice-aware aligner STAR v2.6.1c, or each non-overlapping exon mapped reads are counted.
The sum of all exons yields the number of reads per gene. (samtools v1.8, subread v1.6.1) For analysis of differential expression it is assumed that the reads per gene correlate with the amount of mRNA for this gene in the sample.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: small intestine

extract_protocol:
small intestine were dissected and small intestine epithelial cells was isolated from collagen induced arthritis model, RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: small intestine epithelial cells

value: HIF2[alpha] +/- [delta]IEC

value: collagen induced arthritis model


title: elg1D Brdu 25C 30' MNase rep1 [Alb192_elg1_Brdu_S30]

source_name: elg1D Brdu 25C 30' MNase

value: Brdu


title: Pancreas from Pdx1-Cre+, poh1f/+ mice rep1

last: Wang

value: Pancreas

value: tissue

value: pancreatic cells


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d110 peripheral blood bio rep 2

description: 10x Genomics

source_name: Peripheral Blood


title: Acacetin 3


title: Acacetin 2


title: elg1D BrdU 25C 30' MNase rep2 [Alb882_elg1D_BrdU_S30]

source_name: elg1D BrdU 25C 30' MNase

value: BrdU


title: pol306 PCNA_eSPAN 25C 30' sonication rep1 [Alb653_pol306_PCNA_eSPAN_S30]

value: 25C 30' sonication


title: HU-231027_WT

value: HIF2[alpha] +/- F/F(Littermate control)


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d110 peripheral blood bio rep 1

description: 10x Genomics

value: Peripheral Blood


title: In_vitro_Multiome_Gene_PBS

value: Spleen

value: T cells

value: PBS


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d28 lymph node bio rep 1

description: 10x Genomics

value: Lymph Node


title: HU-231026_delta.Hif2a


title: pol306 PCNA_ChIP 25C 30' sonication rep2 [Alb651_pol306_PCNA_ChIP_S30]


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d201 lymph node bio rep 2

description: 10x Genomics


title: OGD 4

value: BV2 cells

value: OGD


title: HU-231025_WT

value: small intestine epithelial cells


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d110 lymph node bio rep 1

description: 10x Genomics


title: pol306 H3K4me3_eSPAN 25C 30' MNase rep2 [Alb375_pol306_H3K4me3_eSPAN_S30]

source_name: pol306 H3K4me3_eSPAN 25C 30' MNase

value: 25C 30' MNase


title: pol306 H3K56ac_eSPAN 25C 30' MNase rep1 [Alb254_pol306_H3K56ac_eSPAN_S30]

source_name: pol306 H3K56ac_eSPAN 25C 30' MNase


title: OGD 3


title: pol306 BrdU 25C 30' sonication rep1 [Alb605_pol306_BrdU_S30]


title: OGD 2


title: HU-231023_delta.Hif2a

value: HIF2[alpha] +/- [delta]IEC

value: collagen induced arthritis model


title: Acacetin 1

value: Acacetin


title: pol306 Brdu 25C 30' MNase rep1 [Alb252_pol306_Brdu_S30]

source_name: pol306 Brdu 25C 30' MNase

value: Brdu


title: HU-231022_WT


title: pol3079 H3K56ac_eSPAN 30C 45’ HU MNase rep2 [Alb555_pol3079_H3K56ac_eSPAN_S30]

source_name: pol3079 H3K56ac_eSPAN 30C 45’ HU MNase

value: 30C 45’ HU MNase


title: pol306 H3K4me3_eSPAN 25C 30' MNase rep1 [Alb253_pol306_H3K4me3_eSPAN_S30]


title: scRNA-seq and TCR profiling of Homo Spaiens: 350-400 d84 peripheral blood bio rep 2

description: 10x Genomics


title: scRNA-seq and TCR profiling of Homo Spaiens: 350-400 d28 peripheral blood bio rep 1

description: 10x Genomics


title: pol306 BrdU 25C 30' MNase rep2 [Alb374_pol306_BrdU_S30]

source_name: pol306 BrdU 25C 30' MNase

value: BrdU


title: Control 2

value: Control


title: pol3079 H3K4me3_eSPAN 30C 45’ HU MNase rep2 [Alb554_pol3079_H3K4me3_eSPAN_S30]

source_name: pol3079 H3K4me3_eSPAN 30C 45’ HU MNase


title: scRNA-seq and TCR profiling of Homo Spaiens: 350-397 d14 peripheral blood bio rep 1

description: 10x Genomics


title: Control 1


title: pol306 H3K56ac_eSPAN 25C 30' MNase rep2 [Alb376_pol306_H3K56ac_eSPAN_S30]


title: scRNA-seq and TCR profiling of Homo Spaiens: 350-400 d28 peripheral blood bio rep 2

description: 10x Genomics


title: scRNA-seq and TCR profiling of Homo Spaiens: 350-400 d84 peripheral blood bio rep 1

description: 10x Genomics


title: OGD 1


title: scRNA-seq and TCR profiling of Homo Spaiens: 350-117 m6 peripheral blood bio rep 2

description: 10x Genomics


title: Hela.0.ITP.b

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

institute: German Cancer Research Center (DKFZ)

description:
batch_2
Hela.0.ITP

data_processing:
Drop-seq pipeline (v1.0)
picard-2.18.26
STAR-2.6.1
Bcl2Fastq
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count values for each sample

source_name: HeLa

growth_protocol: All cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and and 1% penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was isolated using the NucleoSpin RNA kit. 50–100 ng of RNA in three biological and two technical replicates was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared as described in Parekh et al., 2016.

treatment_protocol: no treatment

value: HeLa

value: human cervix carcinoma cell

value: WT


title: MCF7.0.MTP.b

description:
batch_2
MCF7.0.MTP

value: human breast carcinoma cell


title: MCF7.0.FTP

description:
batch_2
MCF7.0.FTP


title: HelaAJ

description:
batch_2
HelaAJ


title: scRNA-seq and TCR profiling of Homo Spaiens: 368-01a d110 lymph node bio rep 2

description: 10x Genomics


title: Control 3


title: Hela.0.MTP.b

description:
batch_2
Hela.0.MTP


title: pol3079 H3K56ac_eSPAN 30C 45’ HU MNase rep1 [ASC066_pol30-79_S_H3K56ac_eSPAN]


title: Gsdmd-/- [G4]

first: Pin

address: 107 Wenhuaxi Street

institute: Shandong University

data_processing:
Illumina Casava2.19 software used for basecalling.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes count values for each Sample.

source_name: bone marrow macrophages

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: bone marrow macrophages

value: Gsdmd-/-


title: MCF7.0.ITP.b

description:
batch_2
MCF7.0.ITP


title: scRNA-seq and TCR profiling of Homo Spaiens: 350-117 m6 peripheral blood bio rep 1

description: 10x Genomics

value: Peripheral Blood


title: HelaInaO

description:
batch_2
HelaInaO


title: TC71.ITP

description:
batch_1
TC71.ITP

value: human EwS cell


title: Gsdmd-/- [G3]


title: pol3079 H3K4me3_eSPAN 30C 45’ HU MNase rep1 [ASC065_pol30-79_S_H3K4me3_eSPAN]


title: Hela.0.FTP

description:
batch_2
Hela.0.FTP


title: Control 4

value: BV2 cells


title: Gsdmd-/- [G2]


title: TC71.FTP

description:
batch_1
TC71.FTP


title: pol3079 Brdu 30C 45’ HU MNase rep1 [ASC062_pol30-79_S_Brdu]

source_name: pol3079 Brdu 30C 45’ HU MNase


title: scRNA-seq and TCR profiling of Homo Spaiens: 350-397 d14 peripheral blood bio rep 2

description: 10x Genomics


title: scRNA-seq and TCR profiling of Homo Spaiens: 350-117 d28 peripheral blood bio rep 2

description: 10x Genomics


title: pol3079 BrdU 30C 45’ HU MNase rep2 [Alb553_pol3079_BrdU_S30]

source_name: pol3079 BrdU 30C 45’ HU MNase


title: TC71.MTP

description:
batch_1
TC71.MTP


title: Gsdmd-/- [G1]


title: pol3079 PCNA_eSPAN 30C 45' HU sonication rep2 [Alb522_pol3079_PCNA_eSPAN_S45]

value: 30C 45' HU sonication


title: scRNA-seq and TCR profiling of Homo Spaiens: 350-084 d28 peripheral blood bio rep 2

description: 10x Genomics


title: W4-wildtype [W4]

value: wildtype


title: SKNMC.MTP

description:
batch_1
SKNMC.MTP

source_name: SK-N-MC

value: SK-N-MC


title: scRNA-seq and TCR profiling of Homo Spaiens: 350-117 d28 peripheral blood bio rep 1

description: 10x Genomics


title: SKNMC.ITP

description:
batch_1
SKNMC.ITP


title: W3-wildtype [W3]


title: W2-wildtype [W2]


title: SKNMC.FTP

description:
batch_1
SKNMC.FTP


title: pol3079 PCNA_ChIP 30C 45' HU sonication rep1 [Alb406_pol3079_PCNA_ChIP_S45]

source_name: pol3079 PCNA_ChIP 30C 45' HU sonication


title: scRNA-seq and TCR profiling of Homo Spaiens: 350-065 d28 peripheral blood bio rep 2

description: 10x Genomics


title: SKES.MTP

description:
batch_1
SKES.MTP


title: pol3079 BrdU 30C 45' HU sonication rep2 [Alb521_pol3079_BrdU_S45]

source_name: pol3079 BrdU 30C 45' HU sonication


title: W1-wildtype [W1]


title: scRNA-seq and TCR profiling of Homo Spaiens: 350-041 m6 peripheral blood bio rep 2

description: 10x Genomics


title: pol3079 BrdU 30C 45' HU sonication rep1 [Alb407_pol3079_BrdU_S45]


title: SKES.ITP

description:
batch_1
SKES.ITP


title: SKES.FTP

description:
batch_1
SKES.FTP


title: Flow-Sorted e15.5 endocrine-committed and endocrine-progenitor cells-DKO 3

city: Indianapolis

first: Jason

last: Spaeth

state: IN

address: 1210 Waterway Blvd

department: Pediatrics

institute: Indiana University

data_processing:
Cell Ranger 5.0.1 (http://support.10xgenomics.com/) was utilized to process the raw sequence data generated. Briefly, CellRanger used bcl2fastq (https://support.illumina.com/) to demultiplex raw base sequence calls generated from the sequencer into sample specific FASTQ files, and the FASTQ files were then aligned to the mouse reference genome mm10 with RNA-seq aligner STAR. The aligned reads were traced back to individual cells, and the gene expression level of individual genes was quantified based on the number of UMIs detected in each cell.
Seurat (4.3.0.1) was used for downstream analysis. For quality control, genes detected in less than 3 cells, cells with less than 250 expressed genes, cells with less than 500 detected UMIs, cells with greater than 20% mitochondrial gene contents, and cells with log10(the number of genes per UMI per cell) less than 0.8 were filtered out, as these are all parameters of low quality or dying cells. Read counts for each sample were log normalized (feature counts/total counts per cell x 1,000) using Seurat function “NormalizeData”. Data was integrated together using the “FindIntegrationAnchors” and “IntegrateData” functions in Seurat. Data was clustered using k-Nearest Neighbor (KNN) and Louvain modularity optimization algorithm using 25 principal components and resolution of 0.6 via Seurat functions “FindNeighbors” and “FindClusters” respectively. The “FindConservedMarkers” function was subsequently used to identify cell cluster marker genes per cluster. Each cluster was then identified using at least three marker genes curated from the literature and Panglao single cell database. The marker gene plot was visualized “VlnPlot” and “FeaturePlot” functions. Cell clusters were visualized using the Uniform Manifold Approximation and Projection (UMAP) plots.
Differentially expressed genes were determined by Wilcoxon rank sum test among each genotype separately. For Gene Ontology (GO) enrichment analysis, the “clusterProfiler” software package was used to explore the enrichment degree of biological process (BP) of the differentially expressed genes and conserved marker genes within each cluster. The gene SYMBOL was converted to ENTREZID form and GO enrichment analysis was performed. Data visualization was performed with dotplot function.
Assembly: mm10

source_name: e15.5 endocrine progenitor and endocrine committed cells

growth_protocol: Isolated pancreata from e15.5 Control (Neurog3-Cre;Brg1f/+;Brm+/-;R26LSL-tdTomato), Brg1Δendo;Brm+/- (Neurog3-Cre; Brg1f/f; Brm+/-; R26LSLtdTomato) or DKOΔendo (Neurog3-Cre; Brg1f/f; Brm-/-; R26LSLtdTomato) were dispersed into a single cell suspension (Accumax, Sigma A7089), stained with DAPI, and sorted by fluorescence activated cell sorting. Single cell suspensions were then subjected to droplet based scRNASeq

extract_protocol:
Each clean single cell suspension was counted with hemocytometer under microscope for cell number and cell viability. The single cell suspension had a viability of >90%. Approximately 200-1000 targeted cell recovery per sample was applied to a single cell master mix with lysis buffer and reverse transcription reagents, following the Chromium NextGEM Single Cell 3’ Reagent Kits User Guide, CG000204 Rev D (10X Genomics, Inc). Along with the single cell gel beads and partitioning oil, the single cell master mixture containing the single cell suspension was dispensed onto a Single Cell Chip G in separate wells, and the chip loaded to the Chromium Controller for GEM generation and barcoding, followed by cDNA synthesis and library preparation.
At each step, the quality of cDNA and library were examined by Bioanalyzer and Qubit. The resulting barcoded libraries were pooled in equal molarity and sequenced in a custom program for 28 bp plus 91 bp paired-end sequencing on Illumina NovaSeq 6000 sequencer (Illumina, Inc.). Approximately 50000 reads per cell were generated and 91% of the sequencing reads reached Q30 (99.9% base call accuracy). A Phred quality score (Q score) was used to measure the quality of sequencing.


title: pol3079 PCNA_ChIP 30C 45' HU sonication rep2 [Alb520_pol3079_PCNA_ChIP_S45]


title: pol3079 PCNA_eSPAN 30C 45' HU sonication rep1 [Alb408_pol3079_PCNA_eSPAN_S45]


title: Flow-Sorted e15.5 endocrine-committed and endocrine-progenitor cells-DKO 2

value: e15.5 endocrine progenitor and endocrine committed cells


title: scRNA-seq and TCR profiling of Homo Spaiens: 350-041 m6 peripheral blood bio rep 1

description: 10x Genomics


title: pol3079 PCNA_eSPAN 25C 40' sonication rep2 [Alb602_pol3079_PCNA_eSPAN_S40]

source_name: pol3079 PCNA_eSPAN 25C 40' sonication

value: 25C 40' sonication


title: MHH.ES1.MTP

description:
batch_1
MHH.ES1.MTP


title: Flow-Sorted e15.5 endocrine-committed and endocrine-progenitor cells-dEndo 4


title: Flow-Sorted e15.5 endocrine-committed and endocrine-progenitor cells-DKO 1


title: MHH.ES1.FTP

description:
batch_1
MHH.ES1.FTP


title: scRNA-seq and TCR profiling of Homo Spaiens: 350-041 d14 peripheral blood bio rep 1

description: 10x Genomics

source_name: Peripheral Blood


title: scRNA-seq and TCR profiling of Homo Spaiens: 350-041 d14_peripheral blood bio rep 2

description: 10x Genomics


title: pol3079 PCNA_ChIP 25C 40' sonication rep3 [Alb673_pol3079_H3K79me2_ChIP_S40]

source_name: pol3079 PCNA_ChIP 25C 40' sonication


title: MHH.ES1.ITP

description:
batch_1
MHH.ES1.ITP


title: MCF7.2014

description:
batch_1
MCF7.2014


title: pol3079 PCNA_ChIP 25C 40' sonication rep2 [Alb600_pol3079_PCNA_ChIP_S40]


title: Lamina propria, Ulcerative colitis, biol rep 4

city: Seoul

first: Yoonho

last: Lee

address: 88, Olympic-ro 43-gil, Songpa-gu, Seoul, Republic of Korea

department: Department of Biochemistry and Molecular Biology

country: South Korea

institute: University of Ulsan College of Medicine

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Rnager software v6.1.2.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lamina propria of the small bowel

extract_protocol:
Small bowel tissues were rinsed with ice cold 1× phosphate buffered saline, and the mesenteric fat and epithelial layer were mechanically removed. We meticulously isolated the lamina propria-enriched fraction (LP) and the submucosa/muscularis propria-enriched fraction (SM/MP). Curved iris scissors (AC 451/10, Nopa Instruments, Tuttlingen, Germany) were used with precision to dissect within the submucosal layer, following a technique similar to that used in endoscopic submucosal dissection. The dissected LP and SM/MP fractions were minced into small pieces (<1 mm in diameter) and placed in digestion medium (0.05% collagenase IV (Sigma-Aldrich, St. Louis, MO, USA), 0.01% DNase I (Roche, Basel, Swiss) and 10% fetal bovine serum [FBS] in RPMI 1640). Tissues were digested in an incubator at 37°C for 30 min followed by 40 min with 90 rpm agitation for each LP and SM/MP. Dissociated cells were filtered through a 70 µm cell strainer (Falcon, Durham, NC, USA) and washed with RPMI 1640 containing 2% FBS following centrifugation at 400 relative centrifugal force for 10 min. Cell pellets were suspended in RPMI 1640 containing 2% FBS and filtered through a 40 µm cell strainer followed by centrifugation at 400 relative centrifugal force for 10 min. We processed all samples by isolating CD3+ or CD45+ cells using magnetic bead sorting.
We utilized the 10x Genomics Chromium Instrument and cDNA synthesis kit (Chromium Next GEM Single Cell 5ʹ Kit v2 & Chromium Next GEM Chip K Single Cell Kit) to generate a barcoded cDNA library for single Cell RNA-sequencing. cDNA library quality was determined using an Agilent Bioanalyzer.

value: Lamina propria of the small bowel

value: CD3+ T-cells


title: Flow-Sorted e15.5 endocrine-committed and endocrine-progenitor cells-dEndo 2


title: scRNA-seq and TCR profiling of Homo Spaiens: 350-065 d28 peripheral blood bio rep 1

description: 10x Genomics

extract_protocol:
Frozen PBMC samples were thawed, washed once with R10, and then washed with P2. PBMC were counted on a Cellometer Auto 2000 (Nexcelom) and resuspended to a final concentration of approximately 108 cells/mL in P2. Total untouched CD3+ or positively selected CD4+ T cells were enriched using either the EasySep Human T Cell Isolation Kit or the EasySep Human CD4 positive selection kit II, respectively, with the EasyEights magnet (STEMCELL Technologies) all per the manufacturer’s instructions. Following enrichment, T cell populations were washed with P2, re-counted and resuspended in PBS supplemented with 0.05% BSA.
Chromium single cell 5’ v2 gene expression and Chromium single cell V(D)J libraries (10x Genomics) were prepared according to the manufacturer’s instructions without modifications.


title: Submucosa/muscularis propria, Ulcerative colitis, biol rep 4

source_name: Submucosa/muscularis propria of the small bowel


title: Submucosa/muscularis propria, Ulcerative colitis, biol rep 3

value: Submucosa/muscularis propria of the small bowel

value: CD45+ cells


title: Flow-Sorted e15.5 endocrine-committed and endocrine-progenitor cells-dEndo 3


title: Flow-Sorted e15.5 endocrine-committed and endocrine-progenitor cells-dEndo 1


title: pol3079 PCNA_ChIP 25C 40' Sonication rep1 [Alb150_pol3079_PCNA_ChIP_S40]

source_name: pol3079 PCNA_ChIP 25C 40' Sonication

value: 25C 40' Sonication


title: MCF7.2011

description:
batch_1
MCF7.2011

value: WT


title: pol3079 BrdU 25C 40' sonication rep3 [Alb674_pol3079_Input_S40]

source_name: pol3079 BrdU 25C 40' sonication

value: BrdU


title: Lamina propria, Ulcerative colitis, biol rep 3


title: Flow-Sorted e15.5 endocrine-committed and endocrine-progenitor cells-Control 3


title: MCF7.0.ITP.a

description:
batch_1
MCF7.0.ITP

value: human breast carcinoma cell


title: pol3079 BrdU 25C 40' sonication rep2 [Alb601_pol3079_BrdU_S40]


title: Submucosa/muscularis propria, Ulcerative colitis, biol rep 2


title: pol3079 PCNA_eSPAN 25C 40' Sonication rep1 [Alb152_pol3079_PCNA_eSPAN_S40]

source_name: pol3079 PCNA_eSPAN 25C 40' Sonication


title: Hela.0.MTP.a

description:
batch_1
Hela.0.MTP

value: HeLa

value: human cervix carcinoma cell


title: pol3079 BrdU 25C 40' sonication rep1 [Alb151_pol3079_Brdu_S40]


title: Lamina propria, Ulcerative colitis, biol rep 2


title: Flow-Sorted e15.5 endocrine-committed and endocrine-progenitor cells-Control 1


title: Hela.0.ITP.a

description:
batch_1
Hela.0.ITP


title: Submucosa/muscularis propria, Ulcerative colitis, biol rep 1


title: A673.Uta.ITP

description:
batch_1
A673.Uta.ITP

value: human EwS cell


title: Submucosa/muscularis propria, Crohn's disease, biol rep 7


title: MCF7.0.MTP.a

description:
batch_1
MCF7.0.MTP


title: Lamina propria, Ulcerative colitis, biol rep 1


title: pol3079 PCNA_eSPAN 25C 30' sonication rep1 [Alb148_pol3079_PCNA_eSPAN_S30]

source_name: pol3079 PCNA_eSPAN 25C 30' sonication

value: 25C 30' sonication


title: pol3079 PCNA_ChIP 25C 30' sonication rep2 [Alb200_pol3079_PCNA_ChIP_S30]

source_name: pol3079 PCNA_ChIP 25C 30' sonication


title: Mki67-/- Small pre-B 4

city: Melbourne

first: Zhoujie

last: Ding

state: VIC

address: 89 Commercial Road

country: Australia

institute: Monash University

data_processing:
Raw FASTQ files were trimmed with trimmomatic using NexteraPE-PE.fa
Trimmed FASTQ files were aligned to UCSC mm10 genome. Duplicated, mitochondrial and low quality reads were removed.
BAM files were shifted to account for Tn5 cutting sites before MACS2 peak calling (-f BED -q 0.01 --nomodel --shift -75 --extsize 150).
Bigwig tracks were generated with deepTools with RPGC normalization.
Differential analysis was performed using Diffbind (DESeq2 method), and significantly differential regions were filtered by FDR < 0.05.
Assembly: mm10
Supplementary files format and content: bigwig, signal track
Supplementary files format and content: narrowPeak, peaks

source_name: Bone marrow

extract_protocol:
Cells were pelleted at 500xg for 10 minutes at 4 degree. Tagmentation reaction containing 0.02% Digtonin, 0.1% Tween-20, Tagment DNA Enzyme 1, Tagment DNA Buffer and moleular grade H2O in 25 uL volume per sample was added to each of the cell pellet. Tagmentation was performed at 37 degrees for 60min followedd by 30 min digestion with Proteinase-K
DNA samples were first purified by SPRI bead size selection. Libraries were amplified using Kapa HiFi HotStart Polymerase Ready Mix in 50 uL volume with indexing primers. A post-PCR SPRI bead clean up was performed to purify the libraries.

value: Bone marrow

value: lymphoid progenitor cells


title: pol3079 PCNA_eSPAN 25C 30' sonication rep2 [Alb202_pol3079_PCNA_eSPAN_S30]


title: Mki67-/- Small pre-B 3


title: pol3079 PCNA_ChIP 25C 30' sonication rep1 [Alb146_pol3079_PCNA_ChIP_S30]


title: A673.shEF.TG.ITP

description:
batch_1
A673.shEF.TG.ITP


title: A673.TG.ITP

description:
batch_1
A673.TG.ITP


title: pol3079 H3K56ac_eSPAN 25C 30' sonication rep2 [Alb300_pol3079_H3K56ac_eSPAN_S30]


title: Submucosa/muscularis propria, Crohn's disease, biol rep 6


title: A673.MTP

description:
batch_1
A673.MTP


title: Lamina propria, Crohn's disease, biol rep 7


title: Lamina propria, Crohn's disease, biol rep 6


title: A673.shcontrol.TG.ITP

description:
batch_1
A673.shcontrol.TG.ITP


title: Mki67-/- Small pre-B 1


title: WT Small pre-B 4


title: Flow-Sorted e15.5 endocrine-committed and endocrine-progenitor cells-Control 2


title: pol3079 H3K56ac_eSPAN 25C 30' sonication rep1 [Alb186_pol3079_H3K56ac_eSPAN_S30]


title: pol3079 PCNA_eSPAN 25C 40' sonication rep3 [Alb675_pol3079_H3K4me3_ChIP_S40]


title: WT Small pre-B 3


title: WT Small pre-B 2


title: Submucosa/muscularis propria, Crohn's disease, biol rep 5


title: pol3079 H3K4me3_eSPAN 25C 30' sonication rep2 [Alb299_pol3079_H3K4me3_eSPAN_S30]


title: Lamina propria, Crohn's disease, biol rep 5


title: Mki67-/- Small pre-B 2


title: Submucosa/muscularis propria, Crohn's disease, biol rep 4


title: pol3079 H3K4me3_eSPAN 25C 30' sonication rep1 [Alb185_pol3079_H3K4me3_eSPAN_S30]


title: A673.HK.ITP

description:
batch_1
A673.HK.ITP


title: Mki67-/- Pro-B 4


title: pol3079 BrdU 25C 30' sonication rep4 [Alb298_pol3079_BrdU_S30]

source_name: pol3079 BrdU 25C 30' sonication


title: Lamina propria, Crohn's disease, biol rep 4


title: A673.FTP

description:
batch_1
A673.FTP


title: Mki67-/- Pro-B 3


title: A673.KS.ITP

description:
batch_1
A673.KS.ITP


title: Lamina propria, Crohn's disease, biol rep 3


title: A673.DS.ITP

description:
batch_1
A673.DS.ITP


title: pol3079 Brdu 25C 30' sonication rep2 [Alb184_pol3079_Brdu_S30]

source_name: pol3079 Brdu 25C 30' sonication

value: Brdu


title: Submucosa/muscularis propria, Crohn's disease, biol rep 3


title: Mki67-/- Pro-B 2


title: Mki67-/- Pro-B 1


title: Submucosa/muscularis propria, Crohn's disease, biol rep 2


title: pol3079 Brdu 25C 30' sonication rep1 [Alb147_pol3079_Brdu_S30]


title: HDL127_Spleen_TCRG

city: New York City

first: Joshua

middle: Ian

last: Gray

state: New York

address: 630 168th Street

department: CCTI

data_processing:
Raw data were processed using the standard immunoSEQ Analyzer from Adaptive Biotechnologies Corporation.
Assembly: Third party provider description: "Sequences were not aligned against a reference genome; instead they were aligned and annotated based on our custom pipeline using primers designed to IMGT reference V and J genes. The CDR3 regions were defined as per IMGT beginning with the second conserved cysteine encoded by 3’ portion of V gene segment. IMGT reference: Yousfi Monod, M., Giudicelli, V., Chaume, D. & Lefranc, M. P. IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs. Bioinformatics 20, (Suppl 1): i379–i385 (2004).
Supplementary files format and content: Processed data files are in the form of tsv files containing clonal counts, nt and aa sequences, as well as VDJ subtype information

source_name: Spleen

extract_protocol:
DNA was isolated from cell pellets using the DNA micro kit (Qiagen) and DNA concentrations were assessed using the NanoDrop (Thermo Scientific).
Other

value: Spleen

value: gd T cells

tag: developmental stage

value: pediatric


title: A673.ITP

description:
batch_1
A673.ITP


title: pol3079 H3K56ac_eSPAN 25C 30' MNase rep2 [Alb218_pol3079_H3K56ac_eSPAN_S30]

source_name: pol3079 H3K56ac_eSPAN 25C 30' MNase

extract_protocol:
For analysis of DNA replication by BrdU-IP-ssSeq, and PCNA ChIP and eSPAN experiments, chromatin was fragmented by sonication (15 seconds on and 30 seconds off for 10 cycles in a Bioruptor Pico, Diagenode). For analysis of nucleosome occupancy at nascent chromatin, H3K4me3 and H3K56ac ChIP as well as almost all eSPAN experiments except those marked by sonication, chromatin was digested with MNase to map nucleosomes (Wal and Pugh, 2012).
The ssDNA libraries were prepared using the Accel-NGS 1S Plus kit (Cat no. 10096, Swift Bioscience).

value: 25C 30' MNase


title: WT Pro-B 4


title: pol3079 H3K56ac_eSPAN 25C 30' MNase rep1 [ASC072_pol30-79_S30_H3K56ac_eSPAN]


title: Lamina propria, Crohn's disease, biol rep 2

value: Lamina propria of the small bowel

value: CD3+ T-cells


title: HDL127_MLN_TCRG

source_name: MLN

value: MLN


title: Submucosa/muscularis propria, Crohn's disease, biol rep 1

value: Submucosa/muscularis propria of the small bowel


title: pol3079 H3K4me3_eSPAN 25C 30' MNase rep2 [Alb217_pol3079_H3K4me3_eSPAN_S30]

source_name: pol3079 H3K4me3_eSPAN 25C 30' MNase


title: WT Pro-B 2

value: WT


title: HDL127_MLN_TCRAD


title: pol3079 Brdu 25C 30' sonication rep3 [Alb201_pol3079_Brdu_S30]


title: Lamina propria, Crohn's disease, biol rep 1


title: HDL127_Lung_TCRG

source_name: Lung

value: Lung


title: pol3079 H3K4me3_eSPAN 25C 30' MNase rep1 [ASC071_pol30-79_S30_H3K4me3_eSPAN]


title: HDL127_Lung_TCRAD


title: MDA-MB-231 BACH1 KO#3, 0g/L Glc

first: Wei

last: Gu

address: 1130 St. Nicholas Ave.

data_processing:
RTA (Illumina) was used for base calling and bcl2fastq (version 2.19) was used for converting BCL to fastq format, coupled with adaptor trimming.
Pseudoalignment was performed to a kallisto index created from transcriptome Human:GRCh38.p12 using kallisto (0.44.0).
The differentially expressed genes under various conditions were analyzed by DESeq2 R package.
Assembly: hg38
Supplementary files format and content: Excel file that includes the TPM values for each sample

extract_protocol:
Total RNA was isolated using TRIzol (Thermo Fisher Scientific, Cat#15596018) following the manufacturer's instructions.
Library was prepared using the Illumina TruSeq chemistry

value: breast cancer cells

value: BACH1 knockout

value: 0g/L glucose


title: Mki67-/- Pre-pro-B 4


title: pol3079 Brdu 25C 30' MNase rep2 [Alb216_pol3079_Brdu_S30]

source_name: pol3079 Brdu 25C 30' MNase


title: pol3079 Brdu 25C 30' MNase rep1 [ASC070_pol30-79_S30_Brdu]


title: WT Pro-B 1


title: Mki67-/- Pre-pro-B 3


title: MDA-MB-231 BACH1 KO#3, 4.5g/L Glc

value: 4.5g/L glucose


title: HDL127_Spleen_TCRAD


title: HDL127_LLN_TCRAD

source_name: LLN

value: LLN


title: MDA-MB-231 BACH1 KO#2, 0g/L Glc


title: Mki67-/- Pre-pro-B 2

value: Bone marrow

value: lymphoid progenitor cells


title: MDA-MB-231 BACH1 KO#2, 4.5g/L Glc


title: HDL127_LLN_TCRG


title: pol308 PCNA_eSPAN 25C 30' sonication rep2 [Alb693_merge_pol308_PCNA_eSPAN]

source_name: pol308 PCNA_eSPAN 25C 30' sonication

value: 25C 30' sonication


title: WT Pro-B 3


title: Mki67-/- Pre-pro-B 1


title: pol308 PCNA_eSPAN 25C 30' sonication rep1 [Alb658_pol308_PCNA_eSPAN_S30]


title: HDL125_Spleen_TCRG

value: Spleen

value: gd T cells


title: MDA-MB-231 BACH1 KO#1, 0g/L Glc


title: HDL125_Spleen_TCRAD

value: pediatric


title: pol308 PCNA_ChIP 25C 30' sonication rep2 [Alb656_pol308_PCNA_ChIP_S30]

source_name: pol308 PCNA_ChIP 25C 30' sonication


title: WT Pre-pro-B 4


title: MDA-MB-231 BACH1 KO#1, 4.5g/L Glc


title: HDL125_MLN_TCRG


title: pol308 BrdU 25C 30' sonication rep2 [Alb657_pol308_BrdU_S30]

source_name: pol308 BrdU 25C 30' sonication

value: BrdU


title: WT Pre-pro-B 2


title: HDL125_LLN_TCRG


title: pol308 BrdU 25C 30' sonication rep1 [Alb609_pol308_BrdU_S30]


title: WT Pre-pro-B 1


title: WT Pre-pro-B 3


title: pol308 PCNA_ChIP 25C 30' sonication rep1 [Alb608_pol308_PCNA_ChIP_S30]


title: MDA-MB-231 Ctrl#1, 0g/L Glc


title: pol308 H3K56ac_eSPAN 25C 30' MNase rep2 [Alb513_pol308_H3K56ac_eSPAN_S30]

source_name: pol308 H3K56ac_eSPAN 25C 30' MNase

value: 25C 30' MNase


title: MDA-MB-231 Ctrl#2, 4.5g/L Glc


title: MDA-MB-231 Ctrl#1, 4.5g/L Glc


title: HDL125_LLN_TCRAD


title: HDL125_Jejunum_TCRG

source_name: Jejunum

value: Jejunum


title: pol308 H3K4me3_eSPAN 25C 30' MNase rep2 [Alb512_pol308_H3K4me3_eSPAN_S30]

source_name: pol308 H3K4me3_eSPAN 25C 30' MNase


title: HepG2_shKDM1A_IgG_CUTTAG

data_processing:
The sequencing reads obtained from the Illumina platform were subjected to quality control using FastQC (v0.11.9) to assess the quality of the reads.
Adapter trimming and read filtering were performed using Trim-galore (0.6.5-1).
The filtered reads were then aligned to the human genome (UCSC hg38) using Bowtie2 version 2.2.6.
The aligned reads were processed by MACS2 (v2.2.7.1) to call peaks and transformed to bigwig formatted files by bamCoverage function in Deeptools (v3.5.1) with default parameters.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: liver

extract_protocol:
The CUT&Tag experiments were performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech Co., Ltd., TD903) according to the manufacturer’s instructions.
The library was constructed by TruePrep® Index Kit V2 for Illumina kit and PCR amplification

value: liver

value: HCC

value: KDM1A shRNA

value: IgG Abclonal AC005


title: BMMCs, Zc3h12a-RNP, 4

city: Bellinzona

first: Cristina

last: Leoni

state: Ticino

address: Via F. Chiesa 5

department: Molecular Immunology

country: Switzerland

institute: Institute for Research in Biomedicine

data_processing:
Quality control of reads was performed using fastqc v.0.11.9 and RSeQC v.4.0.0 and mapped to reference mouse genome build Mus_musculus.GRCm39.107 using HiSat2 v.2.2.1.
Gene expression counts were generated using featureCounts v.2.0.1 and corrected for batch effect using the removeBatchEffect function in R.
Differential expression analysis was performed using the Omics Playground platform.
Assembly: GRCm39
Supplementary files format and content: *.gene.counts.txt files contain raq read counts for each samples.

source_name: BMMCs

growth_protocol: Total bone marrow was isolated from mouse and cultured in humidified atmosphere with 5% CO2 at 37C for at least 4 weeks in the presence of IL-3 to induce bone marrow-derived mast cell (BMMC) differentiation. BMMCs were transfected with either Zc3h12a or scrambled gRNA-Cas9 RNPs and cultured for 1 week.

extract_protocol:
Cells were resuspended in Trizol and total RNA was extracted with Direct-Zol RNA mini Prep (Zymo Research)
RNA libraries for RNA-seq were prepared using Tecan Revelo mRNA Library Prep Kit following manufacturer's protocols.

value: BMMCs

value: Zc3h12a KO


title: BMMCs, Zc3h12a-RNP, 2


title: HDL125_Jejunum_TCRAD


title: BMMCs, Zc3h12a-RNP, 3


title: pol308 H3K4me3_eSPAN 25C 30' MNase rep1 [Alb367_pol308_H3K4me3_eSPAN_S30]

data_processing:
Raw reads were firstly trimmed by Cutadapt (Marcel, 2011) to remove adapters and low quality reads, and then mapped to the yeast genome (sacCer3) using Bowtie2 (Langmead and Salzberg, 2012).Duplicate reads were further filtered by Sambamba (Tarasov et al., 2015) to remove PCR duplication.
The genome-wide read coverage on Watson and Crick strands were calculated at the bin of 1bp using deepTools bamCoverage (Ramirez et al., 2016). Then, the raw genome-wide read coverage was normalized with the number of total mapped reads to obtain counts per million value (CPM).
Spike-in added samples normalization. For each Sonication-BrdU-IP-ssSeq sample, the raw genome-wide coverage was normalized using the formula: BrdUsoni = (BrdUcov / BrdUspike) / (Inputread / Inputspike). BrdUcov is the raw coverage of BrdU-IP-ssSeq; BrdUspike is the number of total mapped spike-in reads (S. pombe reads) in BrdU sample, Inputread is the number of total mapped reads in input, and Inputspike is the number of total mapped spike-in reads (S. pombe) in input. In this way, BrdU incorporation at each strain was quantified as BrdUsoni.
Spike in added samples normalization. For each MNase-BrdU-IP-ssSeq dataset, reads with the nucleosome sized (120~170bp) were first selected to calculate the raw coverage of nucleosome occupancy surrounding replication origins, and then normalized using the formula: BrdUMNase = (BrdUcov-MNase / BrdUspike-MNase) / (Inputread-MNase / Inputspike-MNase). BrdUcov-MNase is the raw coverage of the nucleosome-sized reads, BrdUspike-MNase is the number of mapped nucleosome-sized spike-in reads in the same sample, Inputread-MNase is the number of mapped  nucleosome-sized reads in input, and Inputspike-MNase is the number of mapped nucleosome-sized spike-in reads in the same input sample. In this way, the nucleosome occupancy on nascent chromatin was quantified as BrdUMNase.
Assembly: saccer3
Supplementary files format and content: tar of bw, bigwig format, CPM which is normalized by total number of reads
Supplementary files format and content: tar of bw, bigwig format, BrdU coverage normalized by spike-in and input described as formulas above.


title: HepG2_shctr_IgG_CUTTAG

value: control shRNA


title: HDL125_MLN_TCRAD

value: MLN


title: MDA-MB-231 Ctrl#2, 0g/L Glc

value: breast cancer cells

value: WT

value: 0g/L glucose


title: SHAGGY_6251 day 21

city: Memphis

first: Michael

last: Dyer

address: 262 Danny Thomas Pl MS 324

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

data_processing:
Trimmed and initial quality control with FastQC.
Aligning and counting with STAR.
Duplicate removal using GATK ‘MarkDuplicates’.
TPM matrices generated using RSEM.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files with raw counts, rpkm and fpkm for each sample
Supplementary files format and content: Tab-delimited text file with all compiled tpm values for all 16 samples.

source_name: Mouse-human xenograft

extract_protocol:
Biopsied tissue underwent RNA extraction using Trizol reagent (Invitrogen). Biopsied tissue was manually homogenized in microcentrifuge tubes using a disposable micro-pestle (Fisher Scientific), and solubilized in 800 mcl Trizol. 200 mcl chloroform was added followed by centrifugation to separate  nucleic acids. The aqueous fraction was collected and RNA was precipatated by the addition of 500 mcl isopropanol and 1 mcl glycogen. Precipirate was pelleted by centrifugation, washed with 75% ethanol, and resolubilized in nuclease-free water.
RNA-sequencing libraries were generated from 250 – 1000 ng of input RNA using the TruSeq Total Stranded RNA Library Kit (Illumina).

value: xenograft tumor

tag: mouse number

value: vehicle control

tag: time point_(days)

value: recurrence

tag: xenograft model


title: HDL124_Spleen_TCRG

tag: tissue

value: Spleen

tag: cell type

value: gd T cells

value: pediatric


title: pol308 BrdU 25C 30' MNase rep2 [Alb511_pol308_BrdU_S30]

source_name: pol308 BrdU 25C 30' MNase

value: 25C 30' MNase

tag: genotype

tag: treatment

value: BrdU


title: HDL124_Spleen_TCRAD

source_name: Spleen


title: pol308 BrdU 25C 30' MNase rep1 [Alb366_pol308_BrdU_S30]

tag: strain


title: BMMCs, Scrambled, 4

value: Zc3h12a WT


title: SHAGGY_6251 day 14


title: BMMCs, Scrambled, 3


title: HDL124_MLN_TCRG


title: SHAGGY_6251 day 7


title: BMMCs, Scrambled, 2


title: SHAGGY_6251 day 3


title: pol308 H3K56ac_eSPAN 25C 30' MNase rep1 [Alb368_pol308_H3K56ac_eSPAN_S30]


title: HDL124_LLN_TCRAD

value: LLN


title: pol3090 H3K4me3_eSPAN 25C 30' MNase rep2 [Alb797_pol3090_H3K4me3_eSPAN_S30]

source_name: pol3090 H3K4me3_eSPAN 25C 30' MNase


title: HDL124_Lung_TCRAD

value: Lung


title: SHAGGY_6251 day 0


title: scRNA-seq and TCR profiling of Homo Spaiens: 350-084 d28 peripheral blood bio rep 1

first: Julian

last: Zhou

address: 425 S. Euclid Ave.

description: 10x Genomics

data_processing:
Sequences were processed using Cell Ranger software version 6.1.2
Assembly: GRCh38
Supplementary files format and content: Each matrix.mtx.gz contains a gene expression count matrix stored in the Market Exchange Format for sparse matrices
Supplementary files format and content: Each features.tsv.gz contains feature information that corresponds to the row indices of matrix.mtx.gz
Supplementary files format and content: Each barcodes.tsv.gz contains cellular barcodes that correspond to the column indices of matrix.mtx.gz
Supplementary files format and content: Each filtered_contig_annotations.csv contains processed and annotated T cell receptors

source_name: Peripheral Blood

value: Peripheral Blood


title: pol3090 H3K4me3_eSPAN 25C 30' MNase rep1 [Alb399_pol3090_H3K4me3_eSPAN_S30]


title: BMMCs, Zc3h12a-RNP, 1

value: BMMCs

value: Zc3h12a KO


title: pol3090 H3K56ac_eSPAN 25C 30' MNase rep2 [Alb798_pol3090_H3K56ac_eSPAN_S30]

source_name: pol3090 H3K56ac_eSPAN 25C 30' MNase


title: SHAGGY_6259 day 21

value: vincristine+irinotecan


title: HDL124_Jejunum_TCRG

value: Jejunum


title: pol3090 H3K56ac_eSPAN 25C 30' MNase rep1 [Alb400_pol3090_H3K56ac_eSPAN_S30]


title: pol3090 BrdU 25C 30' MNase rep2 [Alb796_pol3090_BrdU_S30]

source_name: pol3090 BrdU 25C 30' MNase


title: SHAGGY_6259 day 14


title: HDL124_Jejunum_TCRAD